Given that you are now indicating boot order of HDD/Nvme/USB I presume you have already migrated the system drive to HDD. It is not clear if you also have a Volume(?) on the nvme.
Generally speaking, updating does not affect the data.
1. In theory, the update will not affect hard disk data, but for safety, be sure to back up important data.
I have not had any significant issues with data drives except in circumstances of my own making or where stated in the release notes in advance. I have always updated with drives in place, except when deliberately setting out to break something.
In the case where the system drive is on HDD, The HDD must be installed in order to boot from it/them. I would say that the data drives need to be installed (rather than not). For one, the system would need to see them to confirm they are actually there. Secondly, whether you select nvme or hdd for the system drive, they need to allocate the partition space for the boot/os/swap to exist which makes migration of the system drive possible. The unselected drives are just not active as system drives until and unless migration is activated.
{Caveat: I have no direct knowledge of the -423 devices.}
{Caveat: If data is important to you, there should always be a backup. NOT snapshots, NOT raid, NOR any of the other faux "backups" that exist}
hth